Otto Koloman Wagner was born on July 13, 1841 in the Viennese suburb of Penzing, then still a country village. His father, Rudolf Simeon Wagner (1802-46), a notary to the Royal Hungarian Court, was the son of a master smith and as such socially inferior to his fiancee, Suzanne von Helffenstorffer-Hueber (1806-80). Suzanne's father, who was archivist to the Imperial Court and Army, opposed the match throughout his lifetime and it was only after his death that the couple were at last able to marry.

Otto Wagner was educated by private tutors and French governesses up to the age of nine; he then attended the Akademisches Gymnasium in Vienna for two years before joining the boarding school run by the Benedictines at Kremsmuenster. His mother had decided that her son, a well-built, fair-haired boy with eyes of an intense blue, was to be trained as a lawyer. But Otto hated the life at the boarding school. On one occasion he even ran away and made his own way to Vienna, where his mother had the greatest difficulty in persuading him to return. Much against his will he completed the humanist education which was later to stand him in such good stead as a source of useful slogans. When he was sixteen he studied at the Polytechnic Institute in Vienna. In view of his excellent reports at the Polytechnic Wagner was exempted from military service and was able to proceed at once to the Koenigliche Bauakademie in Berlin, a step advocated by Hansen. In 1861 Wagner returned to Vienna, where he attended the Academy of Fine Arts. In 1863 Wagner completed his studies and won his first competition: for the casino in the Wiener Stadtpark. In the same year Wagner married Josefine Domhart by whom he had three children, Otto, Robert and Susanna. The marriage was unsuccessful and in 1880, shortly after his mother's death, Wagner divorced his wife. In the next year Wagner married Louise Stiffel. In the final period of his first marriage Wagner wrote to Louise: "No matter where I spend my evenings, even when I am engaged in a passionate discussion of artistic questions in the "Kuenstlerhaus", I am always dissatisfied when I return to my moral prison, otherwise known as my home". But he went on to assure her: '' You will find in me all that a true gentleman is capable of. Louise, who was eighteen years younger than himself, Wagner described as ''a creature whom I adore and revere and who, I feel, loves me (loves me as I wish to be loved)''. In 1884 his son Stefan was born, followed in 1885 and 1889 by his daughters Luise and Christine. In 1915, when his wife was taken ill, Wagner started a diary and later that year, after she had died of cancer, his entries gradually took the form of letters; eventually every entry was addressed to his dead wife and closed with "Your Otto" or a similar phrase. One aspect of Wagner's relationship to his wife was the belief that she understood him; this served to strengthen him in his conviction that the turning point in his professional career had also come in his fortieth year. After his wife's death Wagner lived very quietly. By then the war had even crept into his studio, for draughtsmen were in short supply: "I am greatly oppressed by the lack of an assistant. Herr Guenther has almost stopped coming. How am I to finish the church? So far only one design has been inked in and the two perspectives have not even been started." His son, Otto, also a professional architect, was not an ideal assistant: "I have never seen anybody with so little artistic flair and with so little taste. This worries me greatly, for what are all my buildings going to look like if it is left to him to complete them". As a true patriot Wagner was not prepared to buy food on the black market and for long periods he was prone to minor illnesses: "Today I have nothing to eat for my breakfast. And I am supposed to put on weight! I am just skin and bones".

On February 6, 1918 Wagner wrote morosely to his dead wife about a lecture due to be given by Behrens in a few days' time. Meanwhile, Otto Wagner himself had died of erysipelas on April 11. He was buried in the family vault, which he himself had built, in the Hietzing cemetery.